The axle is too short. Axle spacers should have no effect on nut position on the axle. Just slide only the axle with the chain adjusters into the swingarm slots where the axle goes without the wheel, and you should be able to bottom the nut (finger tight) and still get to the cotter pin hole. Remember, the swingarm width is set, and you don't squeeze anything when putting it all together. The spacers allow for proper alignment of the wheel, sprocket and on the "F" model the brake rotor/caliper too. When properly assembled with all the proper parts, the whole assembly including the chain adjusters and the caliper should slide nice and snug between the swingarm sides. No excess play or gaps, and also shouldn't have to be forced either. It's all designed so that things go together without adding stresses to the swingarm or having to improvise.
Steve F